General parameters | annotation.files.dir | output.dir | dataset.info | x.column | short.name.column | group.column | ontology | dict.path | column | denominator.column | tree.path | tree.type | type | MHT.method | cores | Cutoff values | spearman.qvalue.cutoff | pearson.qvalue.cutoff | kendall.qvalue.cutoff | linear_model.qvalue.cutoff | spearman.cor.lower.cutoff / spearman.cor.upper.cutoff | pearson.cor.lower.cutoff / pearson.cor.upper.cutoff | kendall.cor.lower.cutoff / kendall.cor.upper.cutoff | sd.cutoff | cv.cutoff | annotation_size.cutoff | prevalence.cutoff | heterogeneity.cutoff | Advanced configurations | raw_data_sd_filter
This package is considered a duplicate. The official version of this package is found at:https://fcampelo.r-universe.dev/CALANGO
Package: CALANGO 1.0.20
Felipe Campelo
CALANGO: Comparative Analysis with Annotation-Based Genomic Components
A first-principle, phylogeny-aware comparative genomics tool for investigating associations between terms used to annotate genomic components (e.g., Pfam IDs, Gene Ontology terms,) with quantitative or rank variables such as number of cell types, genome size, or density of specific genomic elements. See the project website for more information, documentation and examples, and <doi:10.1016/j.patter.2023.100728> for the full paper.
Authors:
CALANGO_1.0.20.tar.gz
CALANGO_1.0.20.zip(r-4.7)CALANGO_1.0.20.zip(r-4.6)CALANGO_1.0.20.zip(r-4.5)
CALANGO_1.0.20.tgz(r-4.6-any)CALANGO_1.0.20.tgz(r-4.5-any)
CALANGO_1.0.20.tar.gz(r-4.7-any)CALANGO_1.0.20.tar.gz(r-4.6-any)
CALANGO_1.0.20.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CALANGO/json (API)
| # Install 'CALANGO' in R: |
| install.packages('CALANGO', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fcampelo/calango/issues
Pkgdown/docs site:https://labpackages.github.io
Last updated from:a1d14b07c7. Checks:9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 212 | ||
| source / vignettes | OK | 278 | ||
| linux-release-x86_64 | OK | 184 | ||
| macos-release-arm64 | OK | 102 | ||
| macos-oldrel-arm64 | OK | 138 | ||
| windows-devel | OK | 112 | ||
| windows-release | OK | 111 | ||
| windows-oldrel | OK | 116 | ||
| wasm-release | OK | 174 |
Exports:install_bioc_dependenciesmake_reportretrieve_calanguize_genomesretrieve_data_filesrun_CALANGO
Dependencies:apeaskpassassertthatbase64encBiocManagerbriobslibcacachemcallrcliclustercodetoolscolorspacecpp11crosstalkcurldata.tabledendextenddescdigestdownlitdplyrDTeggevaluatefansifarverfastmapfontawesomeforeachfsgclusgenericsggplot2gluegridExtragtableheatmaplyhighrhtmltoolshtmlwidgetshttrhttr2isobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimenlmeopensslotelpbmcapplypermutepillarpkgconfigpkgdownplotlyplyrprocessxpromisespspurrrqapR6raggrappdirsRColorBrewerRcppregistryreshape2rlangrmarkdownS7sassscalesseriationstringistringrsyssystemfontstextshapingtibbletidyrtidyselecttinytexTSPutf8vctrsveganviridisviridisLitewebshotwhiskerwithrxfunxml2yaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Install Bioconductor dependencies | install_bioc_dependencies |
| Prepare and render the HTML5 report | make_report |
| Retrieve calanguize_genomes script from the Github repository | retrieve_calanguize_genomes |
| Retrieve data files from the Github repository | retrieve_data_files |
| Run the CALANGO pipeline | run_CALANGO |
